Learning from Multi-Omics Networks to Enhance Disease Prediction: An Optimized Network Embedding and Fusion Approach

Understanding complex diseases hinges on a profound understanding of intricate biomolecular interactions unfolding within a complex, multidimensional landscape, challenging traditional methods to extract meaningful insights. While multi-omics networks capture the richness of biological data, providing a basis for predicting relationships between biomolecules and various phenotypic traits of complex diseases, their inherent complexity limits their predictive power. To address this challenge, we introduce a novel pipeline that leverages the power of Graph Neural Networks (GNNs) to extract and integrate meaningful information from multi-omics networks. By generating informative node embeddings and seamlessly incorporating them into the original subject-level data, our approach captures both local and global network dependencies, leading to substantial improvements in disease prediction accuracy. The proposed pipeline optimizes the embedding generation process for the specific prediction task, enabling the model to learn task-relevant representations. Through rigorous experimentation, we demonstrate the superior performance of our approach, surpassing existing methods by a substantial margin on nine real-world multi-omics datasets. With remarkable increases in accuracy ranging approximately from 8% to 10% over the best-performing baseline, particularly when the multi-omics networks are moderately dense, striking a balance between capturing complex relationships and avoiding excessive noise. Our findings underscore the potential of GNNs to significantly improve disease prediction by effectively extracting and representing knowledge embedded within multi-omics networks.